title: placenta_HET_hom_F_RRBS_rep6

city: Clayton

first: Patrick

middle: S

last: Western

state: VIC

address: 27-31 Wright Street

department: Centre for Reproductive Health

country: Australia

institute: Hudson Institute of Medical Research

description: PE150 sequencing

data_processing:
Data processing prefomed on the Galaxy Australia Bioinformatics Platform (https://usegalaxy.org.au/)
Sequence files were aligned to the GRC39 (mm39) mouse genome with BWA-meth
Per-base CpG methylation metrics were extracted with MethylDackel with the output limited to CpG sites with a minimum of 5 reads coverage with output presented as CpG methylation fractions
Differentially methylated CpG-rich regions (DMRs) between the groups were identified with Metilene with settings of a minimum of 10 CpGs per DMR and a minimum of 10% methylation difference between groups
Statistically significant DMRs which were below the threshold of Bonferroni adjusted p value of q<0.05 were examined further
DMR regions were visualised and nearby genes and orthologous genome regions identified with the UCSC Genome Browser (https://genome.ucsc.edu/ with Table Browser and LiftOver tools) or Ensemble Biomart (https://asia.ensembl.org/info/data/biomart/index.html).
Assembly: GRC39 (mm39)
Supplementary files format and content: Processed data outputs of MethylDackel analysis showing methylation at each CpG in the genome (.bedgraph files)

source_name: Placenta

growth_protocol: Eedfl/fl mice were crossed with ZP3Cre transgenic mice, facilitating oocyte specific deletion from the primary follicle oocyte stage. For production of placental samples, females producing wild type (Eedfl/fl), heterozygous (Eedwt/del) of homozygous (Eeddel/del) oocytes were mated to isogenic wild type C57bl6 males to produce wild type or heterozygous offspring from oocytes that developed with wild type, heterozygous or homozygous null EED function. These offspring were produced from females producing Eed-wt, Eed-het or Eed-hom oocytes to generate wild type or heterozygous offspring as previously described by Prokopuk, L. et al. Clinical Epigenetics 10, 95 (2018). Heterozygous offspring generated from Eed heterozygous oocytes (HET-het offspring) or from Eed homozygous null oocytes (HET-hom offspring) are isogenic. However, the HET-hom offspring were generated from oocytes that completely lacked functional EED. In contrast, the HET-het offspring were generated from oocytes that had one functional copy of EED. As they are isogenic and heterozygous, comparison of HET-hom with HET-het offspring allowed the identification of differences that resulted from a loss of EED-dependent oocyte programming in the absence of confounding genetic differences. In addition, wild type offspring generated from Eed-het and Eed-wt oocytes allowing the comparison of WT-wt and WT-het offspring with HET-het and HET-hom offspring. This provided controls for differences generated as a result of Eed heterozygosity in offspring.  The mouse lines used were obtained from the following sources: Zp3Cre mice (C57BL/6-Tg 93knw/J; Jackson Labs line 003651, constructed and shared by Prof Barabara Knowles), Eed floxed mice (Eedfl/fl) (B6; 129S1-Eedtm1Sho/J; Jackson Labs line 0022727; constructed and shared by Xie, H. et al. Cell Stem Cell 14, 68-80 (2014). The Eed line was backcrossed to a pure C57BL6/J and shared with us by Associate Professor Rhys Allen and Professor Marnie Blewitt, Walter and Eliza Hall Institute for Medical Research, Melbourne. All subsequent breeding and oocyte collection was performed by the authors at the Hudson Institute of Medical Research / Monash Medical Centre, Clayton, Victoria, Australia. Mice were housed at Monash Medical Centre Animal Facility using a 12-hour light-dark cycle as previously reported by Prokopuk, L. et al. Clinical Epigenetics 10, 95 (2018). Food and water were available ad libitum with room temperature maintained at 21-23°C with controlled humidity. All animal work was undertaken in accordance with Monash University Animal Ethics Committee (AEC) approvals.

extract_protocol:
Placentas were isolated at E17.5, weighed and bisected. Half of the placenta was rinsed in PBS, snap-frozen on dry ice and stored at -80°C for RRBS analysis.  DNA was extracted from 5-6 samples / genotype using Qiagen DNAeasy columns. DNA quality was assessed on agaose gels and samples sent to CD-Genomics for library preparation and sequencing.
Genomic DNA was quantified using the Qubit High Sensitivity assay (Life Technologies). 1 µg of genomic DNA was digested with MspI (NEB), followed by ends preparation, adaptor ligation using Premium RRBS kit (Diagenode). Size selection was performed using AMPure XP beads (Beckman Coulter, Inc.) to obtain DNA fractions of MspI-digested products enriching for the most CpG-rich regions in the range of 150-350 bp. Subsequently, bisulfite treatment was conducted using the ZYMO EZ DNA Methylation-Gold Kit. The converted DNAs were then amplified by twelve cycles of PCR, using 25 μl KAPA HiFi HotStart Uracil+ ReadyMix (2X) and 8-bp index primers with a final concentration of 1 μM each and clean-up using AMPure XP beads. The constructed RRBS libraries were quantified by a Qubit fluorometer with Quant-iT dsDNA HS Assay Kit (Invitrogen), and were sequenced on Illumina Novaseq6000 platform using paired-end 150 bp strategy in CD Genomics (Shirley, NY)

treatment_protocol: Refer to growth protocol for mouse strain information. Mice were crossed to produce genotypes described for each sample.

tag: mouse number

value: Placenta

value: Reduced representation bisulphite sequencing


title: Ctl-2_for_MED30OE

status: Public on May 30 2024

type: SRA

city: La Jolla

first: Chunyu

last: Jin

address: 9500 Gilman Dr. MC0648

country: USA

institute: University of California, San Diego

library_source: transcriptomic

data_processing:
The sequencing reads were trimed by Trim Galore. The adapter sequence to be trimed was selected as “automatic detection” for the first round and the “Illumina small adapters” for the second round(Galaxy Version 0.6.7+galaxy0). Then the reads were mapped to hg38 Refseq database by using Bowtie2 and counted over the entire gene body (transcript) on the sense strand with respect to the gene orientation by using Featurecounts (Galaxy Version 2.0.3+galaxy1). Deseq2 (Galaxy Version 2.11.40.8+galaxy0) was then used to compute the significance of the differential gene expression.
Assembly: hg38
Supplementary files format and content: reads per gene
Library strategy: PRO-seq

molecule: total RNA

organism: Homo sapiens

source_name: MIA PaCa-2

extract_protocol:
For nuclei isolation, cells were incubated with swelling buffer (10 mM Tris-Cl pH 7.5, 2 mM MgCl2 and 3 mM CaCl2) for 5 min on ice and then incubated with lysis buffer (swelling buffer with 0.5% NP-40 and 10% glycerol) for 5 min on ice, before being re-suspended in 100 μl of freezing buffer (50 mM Tris-Cl pH 8.0, 40% glycerol, 5 mM MgCl2 and 0.1 mM EDTA).
For the run-on assay, an equal volume of reaction buffer (10 mM Tris-Cl pH 8.0, 5 mM MgCl2, 300 mM KCl, 1 mM dithiothreitol, 20 units of SUPERase•In, 1% sarkosyl, and 500 μM ATP, GTP, bio-UTP and bio-CTP) was added into each sample before incubation at 30 °C for 5 min. The nuclear run-on RNA was then extracted with TRIzol LS reagent (10296010, Invitrogen) and subjected to hydrolysis, buffer exchange and purification by streptavidin beads (88816, Thermo Fisher). Purified RNA was treated with PNK before being used for complementary DNA synthesis by using the NEBNext Multiplex Small RNA Library Prep Set for Illumina Kit (E7300S, NEB). Obtained complementary DNA template was amplified by PCR using the Phusion High-Fidelity enzyme (M0530L, NEB) for deep sequencing.

tag: cell line

value: MIA PaCa-2

tag: expression


title: WIBR3-E8-r4h

city: Beijing

first: Li

last: Ding

state: Beijing

address: No.5, Yiheyuan Road

country: China

institute: Peking University

description: RNA-seq_primed_wibr3_differentiation.CSV

data_processing:
For PolyA(+) RNA-seq, Trimmomatic software was used to trim the adapters. Hisat2 software was used for the alignment to the hg38 reference genome with default parameters.
The expression count matrix was obtained by FeatureCounts.
Assembly: hg38
Supplementary files format and content: Data were normalized by total mapped reads of each library (CPM: count per million).

extract_protocol:
RNA extracted according to the manufacturer’s instructions.
RNA-seq libraries preparation using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme).

tag: cell type

value: hESC

tag: genotype

value: WT

tag: treatment

value: cultured in E8 medium

tag: time


title: Upf2fl/fl Trp53fl/fl NPCs, AAV9-Cre treatment biol rep#5, 72 hours [UP_C5]

city: Riverside

first: Sika

last: Zheng

state: CA

address: University Ave 900

department: School of Medicine

institute: University of California, Riverside

data_processing:
The raw data was mapped using STAR.
We calculated the gene-level read counts and identified differentially expressed genes by in-house script.
Assembly: mm10

organism: Mus musculus

source_name: Cortex

growth_protocol: For NPCs samples, 200k Upf2fl/fl or Upf2fl/fl Trp53fl/fl NPCs per well were plated in a pre-coated 6 well plate and were cultured in DMEM/F12 media with 1x B27 and 1x penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
72 hours after the infection, media was removed from the well and 1 ml TRIzol was added to each well to extract total RNA following the manufacturer protocol. DNase treatment was performed at 37 ºC for 35 min to degrade residue genomic DNA after TRIzol RNA isolation with 1 unit of Turbo DNase per 10 µg total RNA. Following the DNase treatment, RNA was purified again using phenol-chloroform pH 4.5. RNA concentrations were measured using a Nanodrop 2000c. All samples passed the QC test in the bioanalyzer analysis with a RIN of at least 9.0.
RNA-Seq libraries were constructed using Illumina TruSeq Stranded Total RNA LT Sample Prep kits according to the manufacturer protocol.

treatment_protocol: Mock group was set to add the same volume of NPC media, while Cre group was added with a MOI= 400k in 1 ml NPC media. 14 hours after the plate and infection, AAV contained media was removed and replaced with 2 ml fresh NPC media.

tag: tissue

value: Cortex

value: Neural progenitor cells

value: Upf2fl/fl Trp53fl/fl

value: AAV9-Cre infection

tag: strain background


title: Upf2fl/fl Trp53fl/fl NPCs, AAV9-Cre treatment biol rep#3, 72 hours [UP_C3]


title: MYCOE_1

value: MYCOE


title: Ctl-1_for_MED30OE


title: placenta_HET_hom_F_RRBS_rep5

description: PE150 sequencing

library_source: genomic

molecule: genomic DNA


title: WIBR3-N-MYCP-P13-rep

value: cultured in N-MYCP medium


title: placenta_HET_hom_F_RRBS_rep4

description: PE150 sequencing


title: MIA PaCa-2 cells, MED30_MED30OE_rep#2

data_processing:
bigwig files were generated using the DeepTools “bamCoverage” script integrated in Galaxy server using “Normalized to reads per kilobase per million(RPKM)”.
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&tag

extract_protocol:
cells in culture media were lightly fixed (0.1 % formaldehyde for 2 minutes) for non-histone epitopes or without fixation for histone marks, and quenched glycine of >twice molar concentration of formaldehyde. Next, the cells were washed with PEX buffer (PBS, 2mM EDTA, 0.1% Triton X-100) for 5min thrice, in order to complete remove Mg2+ and permeabilize the cell. Then the cells were blocked by antibody buffer (0.1%BSA, 2mMEDTA) for 10-30min at room temperature, and subjected to primary antibody incubation overnight at 4°C. The antibodies were used as 1:1000 dilution in antibody buffer if not specified. The next day the primary antibody was removed and wash with wash buffer (20mMTrisCl pH7.4, 150mMNaCl, 0.05%Triton X-100) for 5min, and then incubated with secondary antibody 1:2000 diluted in wash buffer for 1h. The secondary antibody contains fluorophore (Alexa FluorTM) so the signal can be checked under microscope. After secondary antibody incubation, cells were washed three times with wash buffer, and then add adapter loaded pAG-Tn5 (purified in-house) in Dig-300 buffer (20mMTrisCl pH7.4, 300mMNaCl, 0.05%Triton X-100) for 1h, followed by three time wash in Dig-300 buffer. Then cells were subjected to tagmentation buffer (10mMMgCl2 in Dig-300 buffer) at 37°C for 1-3h, and terminated and de-crosslinked by adding 7.5ul 0.5MEDTA, 8ul 10%SDS, 0.25ul 20mg/ml proteinase K per 150ul tagmentation buffer in one well and incubated at 65 °C for 30 min, and transferred into Eppendorf tube to avoid evaporation and continue de-crosslinking overnight, followed by DNA purification with DNA purification Kit (Qiagen).
The DNA was eluted and utilized as template for PCR reaction with i7 and i5 dual-index for library construction and sequenced on the NovaSeq 6000 with 100 bp paired-end reads at the UCSD IGM Genomics Center.

tag: antibody

value: MED30(Dr. Thomas G. Boyer, University of Texas Health Science Center at San Antonio)


title: WIBR3-N-MYCP-P2-rep


title: WIBR3-N-MYCP-P8-rep


title: Upf2fl/fl NPCs, No treatment biol rep#9, 72 hours [UM_9]

value: Mock


title: Upf2fl/fl NPCs, No treatment biol rep#6, 72 hours [UM_6]


title: placenta_HET_hom_F_RRBS_rep2

description: PE150 sequencing


title: MIA PaCa-2 cells, MED30_MED30OE_rep#1


title: MIA PaCa-2 cells, MED30_rep#2


title: WIBR3-PXGL-rep

value: cultured in PXGL medium


title: WIBR3-N-MYCP-P13


title: Upf2fl/fl NPCs, No treatment biol rep#5, 72 hours [UM_5]


title: Upf2fl/fl NPCs, No treatment biol rep#4, 72 hours [UM_4]


title: placenta_HET_het_F_RRBS_rep5

description: PE150 sequencing


title: MIA PaCa-2 cells, MED30_rep#1


title: WIBR3-N-MYCP-P11


title: Upf2fl/fl NPCs, No treatment biol rep#3, 72 hours [UM_3]


title: placenta_HET_het_F_RRBS_rep4

description: PE150 sequencing


title: WIBR3-N-MYCP-P10


title: MIA PaCa-2 cells, MED1_MED30OE_rep#2


title: Upf2fl/fl NPCs, No treatment biol rep#8, 72 hours [UM_8]


title: MIA PaCa-2 cells, MED1_MED30OE_rep#1


title: WIBR3-N-MYCP-P2


title: Ctl-2_for_MYCOE


title: Upf2fl/fl NPCs, AAV9-Cre treatment biol rep#8, 72 hours [UC_8]


title: placenta_HET_het_F_RRBS_rep2

description: PE150 sequencing


title: placenta_HET_hom_F_RRBS_rep1

description: PE150 sequencing


title: placenta_HET_het_F_RRBS_rep1

description: PE150 sequencing


title: MIA PaCa-2 cells, MED1_rep#1


title: WIBR3-PXGL


title: MIA PaCa-2 cells, MED30_MED30HAOE


title: Upf2fl/fl NPCs, AAV9-Cre treatment biol rep#4, 72 hours [UC_4]


title: Upf2fl/fl NPCs, AAV9-Cre treatment biol rep#9, 72 hours [UC_9]


title: WIBR3-N-MYCP-P8


title: WIBR3-E-MYCP-P13

value: cultured in E-MYCP medium


title: MIA PaCa-2 cells, MED23_MED30HAOE


title: Upf2fl/fl NPCs, AAV9-Cre treatment biol rep#3, 72 hours [UC_3]


title: placenta_WT_wt_F_RRBS_rep5

description: PE150 sequencing

value: Eedfl/fl


title: placenta_WT_wt_F_RRBS_rep4

description: PE150 sequencing

value: Placenta


title: placenta_WT_wt_F_RRBS_rep3

description: PE150 sequencing

value: Reduced representation bisulphite sequencing


title: WIBR3-E-MYCP-P12


title: placenta_HET_hom_F_RRBS_rep3

description: PE150 sequencing


title: MIA PaCa-2 cells, MED17_MED30HAOE

value: MIA PaCa-2


title: Upf2fl/fl NPCs, AAV9-Cre treatment biol rep#6, 72 hours [UC_6]


title: MIA PaCa-2 cells, MED1_rep#2


title: MIA PaCa-2 cells, MED12_MED30HAOE


title: Upf2fl/fl NPCs, AAV9-Cre treatment biol rep#5, 72 hours [UC_5]


title: placenta_WT_wt_F_RRBS_rep2

description: PE150 sequencing


title: MIA PaCa-2 cells, MED4_MED30HAOE

value: MED4(Dr. Thomas G. Boyer, University of Texas Health Science Center at San Antonio)


title: WIBR3-E-MYCP-P11

value: hESC

value: WT


title: placenta_WT_wt_F_RRBS_rep1

description: PE150 sequencing


title: WIBR3-E-MYC-P5

value: cultured in E-MYC medium without PlaB


title: placenta_HET_het_F_RRBS_rep3

description: PE150 sequencing


title: MIA PaCa-2 cells, MED1_MED30HAOE


title: WIBR3-E-MYCP-P10


title: HUH7_Input

city: Guangzhou

first: Qiangnu

last: Zhang

state: None Selected

address: 1017 Dongmen Bei Lu, 518020Shenzhen, China

institute: Guangzhou Medical University

data_processing:
Data quality control was performed using the fastQC software (Version 0.12.0). The clean data was aligned to a reference genome to obtain comprehensive transcriptomic information. Differential analysis was performed on the IP and Input samples, evaluating based on differential fold change and significance level. Here, we selected genes that were upregulated in the IP relative to the input, using an absolute logFC value > 1.0 and a p-value < 0.05 as criteria, to identify protein-binding genes.
Assembly: hg38
Supplementary files format and content: csv files including RPKM value

source_name: Liver

extract_protocol:
RIP assay was performed using the BersinBioTM RNA Immunoprecipitation (RIP) Kit (BersinBio, Guangzhou). Total RNA from the HUH7 cells  was extracted using Trizol reagent (Thermo Scientific, MA, USA)
The enriched RNA was fragmented using Fragmentation Buffer into short fragments. The fragmented mRNA was then used as a template to synthesize single-stranded cDNA using a random hexamer primer. The double-stranded cDNA was synthesized by adding buffer, dNTPs, and DNA polymerase I. The purified double-stranded cDNA was subjected to end repair, followed by addition of an A-tailing and sequencing adapter treatment. Target-sized fragments were recovered using magnetic beads and amplified through PCR. The constructed libraries were quality-checked using agarose gel electrophoresis. The library concentration was quantified using Qubit 2.0 to ensure suitability for sequencing. Upon passing quality control, different libraries were sequenced on the Illumina sequencer according to the desired effective concentration and target data volume.

value: Liver

value: hepatocellular carcinoma cells


title: PLC_CKO_input

data_processing:
Data quality control was performed using the fastQC software (Version 0.12.0). The quality-controlled sequencing reads were aligned to the reference genome to obtain comprehensive transcriptome information. Peak calling was performed using either exomePeak(version2.0). Differential peak identification between the comparison groups was conducted using the QNB software(version1.0).
Assembly: hg38
Supplementary files format and content: csv files including fold changes of m6A peaks based on normalized counts
Library strategy: MeRIP-Seq

extract_protocol:
Total RNA from the HUH7 and PLC/PRF/5 was extracted using Trizol reagent (Thermo Scientific, MA, USA). The extracted RNA was fragmented using Fragmentation Buffer. m6A Antibody (in kit) was then added, followed by incubation for 4 hours.
Enrichment of mRNA was performed using Oligo d(T) magnetic beads. The mRNA was fragmented into approximately 100bp short fragments using a divalent cation. Immunoprecipitation was carried out using an m6A antibody. The RNA obtained from IP was used as a template to synthesize single-stranded cDNA using a hexamer random primer. Splint adapters were ligated and the resulting products were purified using magnetic beads and amplified by PCR. The constructed library was quality-checked using agarose gel electrophoresis. The library was quantified using Qubit 3.0 to determine if the library concentration was suitable for sequencing. Once the library passed quality control, different libraries were sequenced on the machine according to the required effective concentration and target data output.


title: MIA PaCa-2 cells, MED30


title: WIBR3-E-MYCP-P8


title: PLC_CON_input


title: MIA PaCa-2 cells, MED23


title: PLC_CKO_ip


title: WIBR3-E-MYCP-P7


title: WIBR3-E-MYCP-P9


title: Tia1Nestin-CKO-4

city: Wenzhou

first: Mengxian

last: Jia

state: Zhejiang

address: Nanbaixiang Street

institute: the First Affiliated Hospital of Wenzhou Medical University

description: sample 8

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCh38.107
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: spinal cord

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: spinal cord


title: Tia1Nestin-CKO-3

description: sample 7


title: MIA PaCa-2 cells, MED17


title: Tia1Nestin-CKO-2

description: sample 6


title: HUH7_IP


title: Tia1Nestin-CKO-1

description: sample 5


title: HUH7_CKO_input


title: WIBR3-E8

value: cultured in E8 medium


title: MIA PaCa-2 cells, MED4


title: HUH7_CKO_ip


title: Tia1f/f-3

description: sample 3


title: Tia1f/f-4

description: sample 4


title: MIA PaCa-2 cells, MED1


title: D. melanogaster hmr2, ovaries, small RNA rep2

city: Moscow

first: Alexei

middle: A.

last: Kotov

address: 26 Vavilov Street

country: Russia

institute: Koltzov Institute of Developmental Biology of the Russian Academy of Sciences

library_source: other

data_processing:
For piRNA production analysis adapter sequences were removed by cutadapt 2.8. After quality control with FastQC rRNA, snRNA, snoRNA, and tRNA were filtered from libraries using bowtie (version 1.1.0) with -v 3 parameter. Unaligned reads were then filtered against microRNA set of D. simulans and D. melanogaster obtained from https://ftp.flybase.net/releases/current/dsim_r2.02/ and https://ftp.flybase.net/releases/current/dmel_r6.56/, resrespectively. Small piRNAs of 23–29 nt in length were selected using cutadapt 2.8. This piRNA fraction was mapped to Drosophila transposon canonical sequences v10.1 (https://github.com/bergmanlab/drosophila-transposons/) using bowtie version 1.1.0 with parameters -l 35 -n 3. Mapped reads were counted with htseq-count 2.0.0
Assembly: transposon canonical sequences v10.1 (https://github.com/bergmanlab/drosophila-transposons/)
Supplementary files format and content: piRNA counts for transposon canonical sequences obtained by  htseq-count 2.0.0

molecule: other

organism: Drosophila melanogaster

source_name: ovaries

extract_protocol:
For small RNA libraries preparation RNA was extracted from 0-3 days old gonads of D. melanogaster Hmr2, D. simulans w501 and interspecific hybrids. Small RNA fraction (19-29 nt) was purified by 15% polyacrylamide gel from 20-30 μg total RNA.
Small RNA libraries were prepared using NEBNext Multiplex Small RNA Sample Prep Set for Illumina (#E7300S, NEB) and sequenced on NovaSeq 6000 in 100 bp single-end mode yielding 25-40 million single-end reads per library.

value: ovaries


title: WIBR3-E-MYCP-P5


title: HUH7_CON_input


title: D. melanogaster hmr2, ovaries, small RNA rep1


title: MIA PaCa-2 cells, H3K4me3_MED30HAOE

value: H3K4me3(Cell Signaling#9727)


title: Tia1f/f-2

description: sample 2


title: PLC_CON_ip


title: HUH7_CON_ip


title: D. melanogaster hmr2, ovaries, rep2

data_processing:
RNA-seq libraries of ovaries of hybrids and parental species were pseudo-aligned by kallisto v.0.50.0 (Bray et al., 2016) with following parameters: --single -l 100 -s 0.05. Merged transcriptome sets obtained from NCBI were used as reference (GCF_000001215.4 and GCF_016746395.2 assemblies for D. melanogaster and D. simulans, respectively). Quantified abundances of transcripts for protein-coding genes were imported with tximport v.1.24.0 (Soneson et al., 2015).
Assembly: GCF_000001215.4 and GCF_016746395.2 assemblies for D. melanogaster and D. simulans, respectively
Supplementary files format and content: Summarized transcript-level abundance, estimated counts and transcript lengths in csv format file

molecule: polyA RNA

extract_protocol:
For the preparation of RNA-seq libraries, RNA was isolated from D. melanogaster Hmr2, D. simulans w501 and interspecific hybrid ovaries with TRIzol Reagent (Invitrogen). PolyA selection was done using an Dynabeads™ mRNA Purification Kit (Thermo Fisher Scientific).
RNA-seq libraries were generated using the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina (#E7760, NEB) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1, NEB #E7335, and Set 2, NEB #E7500) according to the manufacturer's instructions and sequenced on the Illumina NovaSeq 6000 SP platform (100 bp runs).


title: MIA PaCa-2 cells, H3K4me3


title: oocytes, Ami3

first: wenbo

last: zhang

state: Guangdong

address: Outer Ring East Road

institute: South China University of Technology

data_processing:
CLC Genomics Workbench y 11.0.1
Sequence reads were trimmed for adaptor sequence/low quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CC genomic benchwork
Assembly: imm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: oocytes

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: oocytes

tag: developmental stage

value: Aged

value: aminophylline


title: oocytes, Ami2


title: E1DE2D.R2C1 replica 3

city: Geneve

first: George

last: Allen

state: Geneve

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

data_processing:
Reads were mapped using Bowtie2 to Pseudomonas aeruginosa PAO1 genome assembly ASM676v1 and counts were aggregated using summarize Overlaps in the package GenomicAlignments in R using the ASM676v1 gtf version 2.2 (NCBI accession: GCF_000006765.1).
Assembly: NC_002516.2
Supplementary files format and content: Excel file of CDS read counts across all samples
Supplementary files format and content: Excel file of CDS RPKMs across all samples

organism: Pseudomonas aeruginosa

source_name: bacteria

growth_protocol: P. aeruginosa strains were cultured at 16°C on LA supplemented with 0.2% arabinose and incubated for 96 hours until colonies became visible.

extract_protocol:
Total RNA was then extracted and purified utilizing the Monarch Total RNA Isolation Kit (New England Biolabs), followed by triple DNase I (Promega) treatment to eliminate any genomic DNA contamination, and subsequently re-purified using a phenol-chloroform extraction method.
Firstly, ribosomal RNA was removed by rRNA removal kit, and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA and performing procedures as follow. Briefly, after fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized and dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

treatment_protocol: Cells were collected and resuspended immediately on RNA protect Bacteria Reagent (QIAGEN) for RNA stabilization.

value: bacteria


title: MIA PaCa-2 cells, K27me2_MED30OE


title: Upf1-cKO, B1-8hi, eLPre, rep2

city: Kyoto

first: Kotaro

last: Akaki

address: Sakyo-ku, Yoshidakonoecho

department: Department of Medical Chemistry

country: Japan

institute: Kyoto University

description: Upf1-cKO, B1-8hi, eLPre, rep2

data_processing:
Control software（MGI Tech）
The acquired reads were trimmed using Trim Galore (https://github.com/FelixKrueger/TrimGalore).
Trimmed reads were aligned to the mouse genome (mm10) using HISAT2 (paired-end, unstranded).
The mapped reads were counted using featureCounts.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: early LPre B cell

growth_protocol: early LPre and sPre B cells were sorted from bone marrow cells by FACS Aria II (BD)

extract_protocol:
Cells were lysed in TRIzol reagent (Invitrogen) and the RNAs were isolated with RNA Clean & Concentrator-5 (Zymo Research).
rRNAs were removed using MGIEasy rRNA Depletion Kit V1.2 (MGI Tech) and cDNA library was prepared using MGIEasy RNA Directional Library Prep Set V2.1 (MGI Tech)

value: early LPre B cell

value: Upf1 Flox/Flox, Mb1 Cre/+, Igh B1-8hi/+


title: Upf1-cKO, B1-8hi, sPre, rep2

description: Upf1-cKO, B1-8hi, sPre, rep2

source_name: sPre B cell

value: sPre B cell


title: MIA PaCa-2 cells, MED12

value: MIA PaCa-2


title: MIA PaCa-2 cells, K27me2


title: E1DE2D.R1C2 replica 3


title: Ctrl, B1-8hi, eLPre, rep2

description: Ctrl, B1-8hi, eLPre, rep2

value: Upf1 Flox/Flox, Mb1 +/+, Igh B1-8hi/+


title: Ctrl, B1-8hi, sPre, rep2

description: Ctrl, B1-8hi, sPre, rep2


title: oocytes, Aged3

value: untreated


title: Upf2fl/fl Trp53fl/fl NPCs, AAV9-Cre treatment biol rep#4, 72 hours [UP_C4]

value: Cortex

value: Neural progenitor cells

value: Upf2fl/fl Trp53fl/fl

value: AAV9-Cre infection


title: MIA PaCa-2 cells, K27Ac


title: Ctrl, B1-8hi, sPre, rep1

description: Ctrl, B1-8hi, sPre, rep1


title: E2D.R1C2 replica 3


title: E2D.R2C1 replica 3


title: D. melanogaster hmr2, ovaries, rep1


title: MIA PaCa-2 cells, IgG_MED30OE_5days

value: Normal Rabbit IgG(Cell Signaling#2729)


title: E1D.R2C1 replica 3


title: MIA PaCa-2 cells, IgG_MED30OE_1day


title: Tia1f/f-1

description: sample 1

value: spinal cord


title: oocytes, Aged1


title: Upf1-cKO, B1-8hi, sPre, rep1

description: Upf1-cKO, B1-8hi, sPre, rep1


title: D32-T315I-ShBcat1

city: Shanghai

first: yu

last: Jiang

address: 280 Chongqing South Road, Shanghai

department: Faculty of Basic Medicine

institute: Shanghai Jiao Tong University School of Medicine

description: 32Dcl3 cell, BCAT1 expression levels were knocked down in 32Dcl3 cells using scramble, RNAseq

data_processing:
RNA was analyzed by NovelBio Co., Ltd. A GO enrichment analysis was performed with the Bioconductor package top GO (https://www.bioconductor.org/)
Assembly: mm10

source_name: cell line

growth_protocol: 32Dcl3 was maintained in RPMI-1640 (Gibco, USA) supplemented with 10% fetal bovine serum (FBS) (Gemini Bio-Products, Inc., Sacramento, USA) and 10% WEHI-3B conditional medium containing IL-3

extract_protocol:
RNA was extracted using RNA Extraction Kits(TIANGEN)， and 5 ug RNA of total RNA was used for the construction of sequencing libraries
And RNA was analyzed by NovelBio Co., Ltd. A GO enrichment analysis was performed with the Bioconductor package top GO (https://www.bioconductor.org/).

treatment_protocol: We knocked down BCAT1 levels in 32Dcl3 cells using a virus-infected approach and collected the cells on day 5 of culture，Scramble and shBcat1 #1 32Dcl3-BCR-ABLT315I cells were sorted by flow cytometry

value: cell line

value: murine myeloid cell line

value: We infected 32Dcl3 cells with shBCAT1


title: Ctrl, B1-8hi, eLPre, rep1

description: Ctrl, B1-8hi, eLPre, rep1


title: E1D.R1C2 replica 3


title: MIA PaCa-2 cells, IgG


title: Upf1-cKO, B1-8hi, eLPre, rep1

description: Upf1-cKO, B1-8hi, eLPre, rep1


title: MIA PaCa-2 cells, K27Ac_MED30OE


title: E1DE2D.E2 replica 3


title: oocytes, Ami1

value: oocytes

value: Aged

value: aminophylline


title: MIA PaCa-2 cells, MYC_MED30OE_5days

value: c-Myc(Cell Signaling#18583)


title: D. simulans w501, ovaries, small RNA rep2

organism: Drosophila simulans

value: ovaries


title: oocytes, Aged2


title: E1DE2D.E1 replica 3

value: bacteria


title: MIA PaCa-2 cells, MYC_MED30OE_1day

value: MIA PaCa-2


title: D. simulans w501, ovaries, small RNA rep1


title: MIA PaCa-2 cells, MYC


title: E1D.E2D replica 3


title: shControl_MEF_S9.6

city: Jinan

first: Can

middle: xin

last: Wen

address: 44 West Wenhua Rd

department: Center for Reproductive Medicine

institute: Shandong University

data_processing:
The library preparations were sequenced on Illumina Novaseq platform at Novogene Science and Technology Co., Ltd (Beijing, China) and 150bp paired-end reads were generated
The read sequences produced by the Illumina pipeline in FASTQ format were pre-processed through Trimmomatic software, and all low-quality reads and PCR adapters were removed
High-quality mapped reads (MAPQ > 30) reads were aligned to the UCSC mm10 genome or hg38  genome using Bowtie2.
All peak calling was performed with MACS2 v2.1.2 using ‘macs2 -q 0.05 --call-summits --nomodel --shift -100 --extsize 200 --keep-dupall’.
bigWig files were generated using the genomicRanges R package. narrowPeak files were generated using MACS v2.1.2 with default settings.
Assembly: mm10；hg38
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak
Library strategy: CUT&Tag

source_name: MEF

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37℃ at 5% CO2.

extract_protocol:
The genomic DNA was extracted by the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech, China).
CUT&Tag libraries were prepared using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech, China). Libraries were amplified using TruePrep Index Kit V2 for Illumina (Vazyme Biotech, China) at 11 cycles on the thermocycler. Libraries were purified with the VAHTS DNA Clean Beads (Vazyme Biotech, China) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: MEF

value: Mouse embryo fibroblasts

value: control

value: S9.6 antibody used


title: D. simulans w501, ovaries, rep2


title: shDdx5_MEF_S9.6

value: Ddx5 knockdown


title: E2D replica 3


title: D. simulans w501, ovaries, rep1


title: E1D replica 3


title: D32-T315I-SCR

description: 32Dcl3 cell, 32Dcl3 cells were infected with Scramble (control virus)., RNAseq

value: We infected 32Dcl3 cells with Scramble (control virus)


title: JSC18-1 5-FU-2 (3)

city: Koto-ku

first: Ayane

last: Nakamura

state: Tokyo

department: Cancer Chemotherapy Center

institute: Japanese Foundation for Cancer Research

data_processing:
Raw FASTQ file were checked quality using FastQC (version 0.11.9) and removed adapters using Trimmomatic (version 0.39).
The reads were aligned to hg38 or mm39 using STAR (version 2.7.9a).
Gene expression was quantified using FeatureCounts of Subread package (version 2.0.1).
Filtering and normalization of low-expression genes were performed using edgeR (version 3.42.2).
Expression of each RNA was converted to counts per million (CPM).
Assembly: hg38 or mm39
Supplementary files format and content: tab-delimited text file include raw counts for each sample.

growth_protocol: JSC15-3 cells were cultured in ACL4/F12 (1:2) medium (Nacalai Tesque, Kyoto, Japan) with 5% heat-inactivated fetal bovine serum (FBS) and 100 μg/mL kanamycin (Meiji Seika Pharma, Tokyo, Japan). JSC18-1 cells were cultured in ACL4/RPMI (1:2) medium with 5% heat-inactivated FBS and 100 μg/mL kanamycin.

extract_protocol:
(1) JSC18-1 cells were treated with or without 5-FU at IC50 values, 1 μM for 5 days, and (2) JSC15-3 and JSC18-1 cells were treated with or without 5-FU at IC50 values, 1 μM and 0.5 μM for 14 days, and (3) their xenograft tumors in BALB/c-nu mice were treated with PBS or 5-FU (100 mg/kg). RNA was extracted using RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
Sequence libraries were constructed with TruSeq stranded mRNA library preparation kit(Illumina) according to the manufacture's instructions.

treatment_protocol: For in vitro samples, JSC18-1 cells were treated with 5-FU at IC50 values, 1 μM for 5 days. JSC15-3 and JSC18-1 cells were treated with 5-FU at IC50 values, 1 μM and 0.5 μM for 14 days. For in vivo samples, their xenograft tumors in BALB/c-nu mice were treated PBS or 5-FU (100 mg/kg).

value: gastric cancer patient-derived cells

value: Treatment of 5-FU (100mg/kg)


title: WT replica 3

value: WT


title: JSC18-1 5-FU-1 (3)


title: Mouse embryo fibroblasts, Mcm8 knockout3

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two groups (three biological replicates per group) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

value: Mcm8 knockout


title: JSC18-1 Vehicle-2 (3)

value: Treatment of PBS


title: JSC18-1 Vehicle-1 (3)


title: Mcm8_WT_MEF_S9.6

value: Mcm8 wildtype


title: Mouse embryo fibroblasts, Mcm8 knockout2


title: E1DE2D.R2C1 replica 2


title: Ctrl-2

city: Los Angeles

first: Xiuju

last: Wu

address: 650 Charles Young Dr East, CHS A2-237

institute: University of California, Los Angeles

data_processing:
Spliced Transcripts Alignment to Reference (STAR, version 2.7.10a)
FASTQ files were generated using bcl2fastq2 software
Sequence reads from each sample were mapped to mouse genome (GRCm39) using Spliced Transcripts Alignment to Reference (STAR, version 2.7.10a) with the default parameters.
Number of reads per gene were counted while mapping with --quantMode GeneCounts option.
Normalized gene counts were generated using R package DESeq2 (version 1.36.0).
Assembly: GRCm39
Supplementary files format and content: comma-separated values files include normalized number reads per gene for each sample

source_name: Brain tdTomato+

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of RNA libraries.
RNA libraries for sequencing were constructed using KAPA Stranded mRNA-Seq Kit (Roche) following manufacturer's protocols.

value: Brain tdTomato+

value: No Tamoxifen


title: JSC15-3 5-FU-2 (3)


title: Mouse embryo fibroblasts, Mcm8 knockout1


title: Ctrl-1


title: Treated_1

value: Tamoxifen treated


title: E1DE2D.R1C2 replica 2

value: bacteria


title: JSC15-3 5-FU-1 (3)


title: P3

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

data_processing:
FASTQ files for each sample were generated using the bcl2fastq software (Illumina Inc.)
Reads were used for annotation against equine, bovine, and human mature and precursor miRNAs listed in the mirBase database (release 22)
Raw expression data were normalized using the trimmed mean of M-values normalization method (TMM normalization) and presented as TMM-adjusted Counts Per Million (CPM)
The differential expression analysis was done using the DESeq2 statistical software package
Assembly: mirBase database (release 22), against equine, bovine, and human mature and precursor miRNAs
Supplementary files format and content: xlsx file include CPM values for each sample

organism: Ceratotherium simum

source_name: Follicular Fluid

extract_protocol:
EVs were isolated using the dual-ended approach of ultracentrifugation followed by precipitation and elution through size exclusion chromatography columns. Initially, in three technical replicates, frozen-thawed collections containing 2 mL of follicular fluid aspirate from individual animals were subjected to an initial ultracentrifugation using an SW 55Ti rotor on the Optima XE-90 Ultracentrifuge (Beckman Coulter; Pasadena, CA, USA.) system at 120,000 xg for 70 min at 4°C, Pelletized EVs were then washed using 3 mL of Dulbecco’s Phosphate Buffered Saline without calcium and magnesium chloride (DPBS (1X)) (Sigma-Aldrich; St. Louis, MO, USA.) and ultracentrifuged once more under the same parameters. Following ultracentrifugation, washed EV pellets were resuspended in Exo-spin™ Buffer and left to precipitate overnight at 4°C prior to being processed through Exo-spin™ mini columns (CELL guidance systems; St. Louis, MO, USA.) according to the manufacturer’s protocol. Ensuing 180 µL EV aliquots were then stored at -80°C for RNA extraction.
Small-RNA libraries were prepared for next-generation sequencing (NGS) using a TruSeq Small RNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

value: Follicular Fluid

value: Extracellular Vesicles

tag: follicle stage

value: Pre-ovulatory


title: JSC15-3 Vehicle-2 (3)


title: E2D.R1C2 replica 2


title: Mouse embryo fibroblasts, wildtype3

value: MEF

value: Mouse embryo fibroblasts

value: wildtype


title: Treated_2


title: P2


title: MEF_No_antibody

value: no primary antibody used


title: Mouse embryo fibroblasts, wildtype2


title: E1D.R2C1 replica 2


title: P1


title: JSC15-3 Vehicle-1 (3)

value: gastric cancer patient-derived cells


title: Mcm8_KO_MEF_S9.6

value: S9.6 antibody used


title: Mouse embryo fibroblasts, wildtype1


title: E1DE2D.E2 replica 2


title: E1D.R1C2 replica 2


title: JSC18-1 5-FU day-14 (2)

value: Treatment of 5-FU for 14 days


title: MedLN

city: Rehovot

first: Jingjing

last: Liu

address: Herzl 234

country: Israel

institute: Weizmann Institute of Science

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
FASTQ files were aligned to the mouse mm10 reference genome using 10x Genomics Cell Ranger software v5.0.1.
The UMI count matrix was converted to Seurat objects using R package Seurat.
SCTransform function was used to normalize each dataset.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: mediastinal lymph nodes

extract_protocol:
Transferred GFP+ B1-8hi B cells were sorted into a cooled 15 mL tube with 0.04% BSA in PBS using a Sony SH800 cell sorter.
12,000 sorted cells suspension was loaded onto Next GEM Chip G targeting 8000 cells and then ran on a Chromium Controller instrument to generate GEM emulsion. Single-cell 3’ RNA-seq libraries were generated according to the manufacturer’s protocol (10x Genomics Chromium Single Cell 3’ Reagent Kit User Guide v3/v3.1 Chemistry). Final libraries were quantified using NEBNext Library Quant Kit for Illumina (NEB) and high sensitivity D1000 TapeStation (Agilent). Libraries were pooled according to targeted cell number, aiming for ~20,000 reads per cell. Pooled libraries were sequenced on a NovaSeq 6000 instrument using an SP 100 cycles reagent kit (Illumina).

treatment_protocol: The host WT mice were transferred with GFP-B1-8hi B cells and tomato CD4+ OT-II T cells followed by NP-OVA+MPLA intranasal immunization, then the NALT and MedLN were collected at day 5 after immunization.

value: mediastinal lymph nodes

value: Transferred GFP+ B1-8hi B cells

tag: strain

tag: age

value: 8-12 weeks

value: wild type

value: NP-OVA+MPLA intranasal immunization


title: E2D.R2C1 replica 2


title: JSC18-1 DMSO day-14 (2)

value: Treatment of DMSO for 14 days


title: D3

value: Dominant


title: D2

value: Follicular Fluid


title: JSC15-3 5-FU day-14 (2)


title: NALT

description: 10x Genomics

source_name: nasal-associated lymph nodes

value: nasal-associated lymph nodes


title: E1DE2D.E1 replica 2

value: bacteria


title: E1D.E2D replica 2


title: KO

city: Osaka

first: Xin

last: Sun

address: 3-1 Yamadaoka, Suita

institute: IFReC, Osaka University

description: 10x Genomics

data_processing:
Cell ranger (version 6.0.0; 10x Genomics) was used to process single-cell data. In brief, cellranger mkfastq was used to output FASTQ files. Sequencing reads in FASTQ files were aligned to the mm10 Mouse genome using cellranger count and gene-by-cell matrices were generated for downstream analysis. Gene-by-cell matrices were analyzed using Seurat (R package, version 4.1.1) and other packages.
We normalized the count data with NormalizeData and selected the top 5,000 highly variable features. Features were scaled with ScaleData and principal component analysis (PCA) was calculated with RunPCA. The top 20 principal components were used to obtain Uniform Manifold Approximation and Projection (UMAP) scatterplots.
Clustering analysis was performed using the top 20 principal components to generate an SNN graph with FindNeighbors, and clusters were identified with the Leiden algorithm implemented in FindClusters with resolution of 0.6. Cluster-specific markers were identified using FindAllMarkers to select differentially expressed genes between each cluster and the average of all remaining clusters with the Wilcoxon Rank Sum test.
Differentially expressed genes were selected with an adjusted p-value cutoff of 0.01 and log2 fold change of 1.0 in absolute value (equivalent to a twofold change). For the integration of datasets, batch correction was performed with RunCanek from the Canek package (R package, version 0.2.1) using the top 5,000 highly variable features in each dataset.
Assembly: mm10
Supplementary files format and content: h5

source_name: spleen

extract_protocol:
Sorted splenic NK cells were washed twice with PBS and suspended in PBS supplemented with 400 μg/mL non-acetylated bovine serum albumin (Sigma Aldrich, B6917).
Individual cells were then coupled to beads using the 10X Genomics Chromium controller (10X Genomics). Single-cell sequencing libraries were prepared following the 10X Genomics Protocol using 5’ Reagent Kits v2 chemistry and sequenced to a median depth of approximately 20,000 reads per cell using an Illumina NovaSeq 6000 on rapid run.

value: spleen

value: NK cells

value: KO


title: JSC15-3 DMSO day-14 (2)


title: G3

value: Extracellular Vesicles

value: Growing


title: E2D replica 2


title: D1


title: WT

description: 10x Genomics

value: WT


title: JSC18-1 DMSO day-5 (1)

value: gastric cancer patient-derived cells

value: Treatment of DMSO for 5 days


title: G2


title: JSC18-1 5-FU day-5 (1)

value: Treatment of 5-FU for 5 days


title: E1D replica 2


title: Ly6GMacs - Multiplexing capture

city: Liège

first: Thomas

last: Marichal

address: Avenue de l'Hopital 11

department: GIGA Institute

country: Belgium

institute: University of Liege

description: The samples were multiplexed together to obtain 2 library: Gene expression and multiplexing capture

data_processing:
The Cell Ranger (v6.1.2) application (10x Genomics) was then used to demultiplex the BCL files into FASTQ files (cellranger mkfastq), to perform alignment (to Cell Ranger mouse genome references 6.1.2 GRCm38/release 102), filtering and unique molecular identifier counting and to produce gene-barcode matrices. The cells from pooled hashtag-labeled samples were at the same time demultiplexed with the barcode detected in each cell (cellranger multi)
Filtered matrix files were used for further scRNA-seq  analyses with R Bioconductor (3.17) and Seurat
Assembly: GRCm38
Supplementary files format and content: barcode sequences corresponding to column indices
Supplementary files format and content: tsv files containing for each feature the feature ID, the name and the type of features (Gene, antibody)
Supplementary files format and content: mtx files describing hte count of genes for all cells

source_name: Lung

extract_protocol: Libraries compatible with Illumina sequencers were generated using Chromium Next GEM Single Cell 3ʹ v3 .1. Hashtag were added using TotalSeq™-B antibodies. The libraries were sequenced on an illumine NovaSeq sequencer with a kit NovaSeq SP100 V1.5 (38% of a total run).

treatment_protocol: C57bl/6 mice were infected by intranasal instillation of 5 PFU of IAV H1N1 PR8/34

value: Lung

value: 9-10 weeks

value: Pooled with 2 conditions:B0301:Mock B0302 and B0303 :IAV


title: WT replica 2


title: G1


title: Ly6GMacs - Gene Expression

description: The samples were multiplexed together to obtain 2 library. Which mean that the input cells and the processed files are the same for the 2 library


title: KO_tumor

description: 10x Genomics

source_name: tumor suspension

extract_protocol:
Sorted TIL-NK cells and tumor suspension from Reg-1fl/fl and Reg-1ΔNK were washed twice with PBS and suspended in PBS supplemented with 400 μg/mL non-acetylated bovine serum albumin (Sigma Aldrich, B6917).
Individual cells were then coupled to beads using the 10X Genomics Chromium controller (10X Genomics). Single-cell sequencing libraries were prepared following the 10X Genomics Protocol using 5’ Reagent Kits v2 chemistry and sequenced to a median depth of approximately 20,000 reads per cell using an Illumina NovaSeq 6000 on rapid run.

value: tumor suspension


title: scRNA_seq_Telogen

city: Lanzhou

first: qingbo

last: zheng

address: No.335, Jian 'gouyan, Xiaoxihu, Qilihe District, Lanzhou City, Gansu Province

institute: Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences

description:
Skin tissue from scapula of yak during hair follicle telogen for single cell RNA sequencing
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Yak, LU_Bosgru_v3.0
Supplementary files format and content: Tab-separated values files and matrix files

organism: Bos grunniens

source_name: skin

extract_protocol:
Skin tissue was collected from the scapular telogen of healthy Tianzhu white yak about 2 years old. After cleaning and disinfection, the skin tissue was washed twice with PBS and 75 % ethanol, and cut into 0.5 × 0.2 cm strips. The skin tissue was digested with 0.25 % disperse enzyme in 37 ° C incubator for 2 hours, and the single hair follicle was pulled out. After digestion with 0.25 % trypsin for 0.5 hours, cells were observed under a microscope to see if they all fell off the hair shaft. After repeated blowing, the cells were filtered and centrifuged by 40 μm cell sieve, and the cells were resuspended by DMEM.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: skin

value: hair follicle

value: telogen


title: E1DE2D.R2C1

value: bacteria


title: E1DE2D.R1C2


title: WT_tumor

description: 10x Genomics


title: KO_NK

description: 10x Genomics


title: E2D.R2C1


title: DMD2_Cln7_Replicate 3

city: Minneapolis

first: Neha

last: Dhoke

state: Minnesota

address: 2231 6th St SE

institute: University of Minnesota

data_processing:
Reads were trimmed using Trimmomatic (v0.33) and quality control on raw reads was performed with fastq.gzC(v0.11.9) (mean quality score 36) was assessed.
STAR(v2.7.3a) was used to align to human (hg38)  reference genomes.
Aligned reads were counted for gene associations using the CHURP pipeline
Differentially expressed genes were identified using edgeR (v3.42.4, negative binomial)
Assembly: hg38
Supplementary files format and content: Comma separated value text files of raw counts for each sample (.txt) -mapped to human genome

source_name: In vitro myotube

growth_protocol: WT,patient derived DMD iPSCs (DMD1 and DMD2) and their CRISPR corrected counterparts (DMD1-Cln25 and DMD2-Cln7) were  transduced with PAX7 and then terminally differentiated into in vitro myotubes. The terminally diffrerentiated myotubes  were collected for RNA isolation)

extract_protocol:
Total RNA was isolated from in vitro terminally differentiated myotubes from  WT, patient derived DMD iPSCs (DMD1 and DMD2) and their CRISPR corrected counterparts (DMD1-Cln25 and DMD2-Cln7).TRIzol (Invitrogen) and the PureLink RNA mini kit (Invitrogen) with on-column DNaseI treatment following the manufacturer’s recommendations.
500 ng of total RNA was used to for generate unique dual-indexed (UDI) TruSeq stranded mRNA libraries.

value: In vitro myotube

value: iPSC-derived myotubes

tag: mouse strain

value: terminal differentiation


title: DMD2_Cln7_Replicate 1


title: DMD2_Cln7_Replicate 2


title: WT_NK

description: 10x Genomics

value: NK cells


title: E2D.R1C2


title: Rhesus Macaque DHFi collected at d28

type: RNA

city: Salvador

first: Eduardo

last: Fukutani

state: Bahia

address: Marginal da - Av. Luís Viana Filho, 3230 - Imbuí, Salvador - BA

country: Brazil

institute: Fundação Oswaldo Cruz

hyb_protocol: Non applicable

scan_protocol: Digital mRNA gene expression analysis was performed with the Nanostring nCounter NHP Immunology panel V2 (Cat # 115000276).

data_processing: Raw read counts were obtained from RCC files using the nSolver 4.0 Data Analysis software and the NS_NHP_Immunology_V2.0 rlf file references included with the nCounter NHP Immunology panel V2 kit.

label: Non applicable

organism: Macaca mulatta

source_name: Cryopreserved Bronchoalveolar lavage (BAL) cells collected at days 0, 3, 7, 14 and 28-35 (necropsy) post-infection

label_protocol: Non applicable

extract_protocol: Cryopreserved BAL cells from pre-infection (d0) and days 3, 7, 14, and 28-35 post infection (necropsy) were thawed and homogenized using Qiagen RLT buffer Plus (Cat # 1053393) and QIAShredder Columns (Cat # 79656). RNA was isolated using the Qiagen RNeasy Mini kit (Cat # 74134) according to manufacturer’s instructions and eluted in 25uL of RNase free water. RNA was concentrated to 25-50ng/uL using Eppendorf Vacufuge plus centrifuge concentrator. RNA quality was confirmed with Agilent TapeStation. RNA was sent to the National Cancer Institute (NCI) Center for Cancer Research Genomics Core at the Frederick National Laboratory.

tag: animal id

value: DHFi

tag: time point

value: aIFNg


title: Rhesus Macaque DHFi collected at d7


title: KO_Sti, rep 3, RNAseq

data_processing:
Quality control of sequenced reads was assessed by FastQC (version 0.11.9).
Sequencing reads were aligned to the mouse reference genome (mm10) using STAR (version 2.7.8a). Aligned reads were counted using summarizeOverlaps from the GenomicAlignments Bioconductor package.
Counts were loaded into R and analyzed with the edgeR and limma packages. Genes were filtered to have at least 10 CPMs (counts per million) in two samples.
Library normalization factors were computed with the TMM method. A design matrix was used containing a group variable composed of the background (WT or KO) or stimulus (Ctl or Sti) status. The voom method implemented in the limma package was used with this design matrix to estimate the mean variance trend.
A linear model was fitted with lmFit function.
Assembly: mm10
Supplementary files format and content: count.rds

source_name: Spleen

extract_protocol:
Total RNA was isolated by miRNeasy Micro kit (QIAGEN).
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio) according to the manufacturer’s instructions.

value: Spleen

value: KO

value: stimulated with IL12/18


title: DMD2_ Replicate 3


title: E1D.R2C1


title: DMD2_ Replicate 2


title: KO_Sti, rep 2, RNAseq


title: Rhesus Macaque DHFi collected at d3


title: E1D.R1C2


title: DMD2_ Replicate 1


title: E1DE2D.E2


title: Rhesus Macaque DHFi collected at d0


title: DMD1-Cln25_Replicate 3

value: iPAX7-DMD1_Cln 25


title: KO_Ctl, rep 3, RNAseq

value: control


title: KO_Sti, rep 1, RNAseq


title: Rhesus Macaque DHNL collected at d14

value: DHNL


title: E1DE2D.E1


title: Rhesus Macaque DHFi collected at d14


title: DMD1-Cln25_Replicate 2


title: Rhesus Macaque DHNL collected at d7


title: KO_Ctl, rep 2, RNAseq


title: KO_Ctl, rep 1, RNAseq


title: E2D


title: DMD1-Cln25_Replicate 1


title: DMD1 Replicate 3


title: E1D.E2D


title: Rhesus Macaque DHNL collected at d0


title: Rhesus Macaque DHNL collected at d3


title: E1D


title: DMD1_Replicate 2


title: WT_Sti, rep 3, RNAseq

value: WT


title: WT


title: WT_Sti, rep 2, RNAseq


title: DMD1_ Replicate 1


title: WT_Sti, rep 1, RNAseq


title: Rhesus Macaque DHAI collected at d7

value: DHAI


title: K562, SSRP1-dTAG, MNase-seq, dTAG7, rep2, 4h

city: Göttingen

first: Kristina

last: Žumer

address: Am Faßberg 11

department: Department of Molecular Biology

country: Germany

institute: Max Planck Institute for Multidisciplinary Sciences

data_processing:
MNase-seq reads were trimmed with Cutadapt  with options: -f fastq -q 30 -m 25 -O 13 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT, followed by mapping to the human genome version GRCh38 merged with the D. melanogaster genome version Dm6 with the Bowtie2 mapper ref with options: --no-unal --no-mixed --no-discordant --very-sensitive --seed 123 --threads 24. Duplicates were marked with Picard tools. We then kept only uniquely mapped and properly paired reads for the downstream analyses. The counts mapping to the spike-in genome were below 1 % and were therefore not used for normalization. We corrected for differences in library sequencing depth with normalization factors based on numbers or reads that mapped to non-transcribed regions in the human genome. These normalization factors were then used for normalization of the human gene counts and coverage profiles. We took the midpoints of the fragments to get the positions of the putative nucleosome dyads. The dyad positions were then smoothed using normal kernel density smoothing with a bandwidth of 75 bp. These smoothed dyad coverages were then used to generate metagene profiles.
Assembly: GRCh38
Supplementary files format and content: bigwig

source_name: genome edited K562

growth_protocol: Cells were subcultured in RPMI medium (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific) and 1x GlutaMax (Thermo Fisher Scientific) and maintained at densities between 1.5x105 and 7x105 cells/ml

extract_protocol:
After centrifugation and washing the cells with cold DPBS we resuspended the cells in 120 μl hypotonic buffer (10 mM HEPES pH 7.4, 2 mM MgCl2 and 0.5 % NP40; supplemented with protease inhibitor cocktail (Sigma)) on ice and incubated 5 minutes. Next we added 0.4 µl micrococcal nuclease (NEB), heated up to 37 °C, added CaCl2 to a final concentration of 2 mM and incubated at 37 °C for 4 minutes before adding one volume of 2x Stop solution containing 20 mM Tris–HCl pH 8, 4 mM MgCl2, 300 mM NaCl, 20 mM EDTA, 3 mM EGTA, 2 % SDS, 0.2 μg/μL RNase A, and 3 ng/µl D.melanogaster mononucleosomes (spike-in DNA). The samples were then incubated at 37 °C for 30 minutes, followed by addition of 200 µg proteinase K (Thermo Scientific) and 15 minutes of incubation at 55 °C. The DNA fragments were then purified by phenol:chloroform:IAA extraction and precipitation with isopropanol.
NGS libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB)

treatment_protocol: 2 million cells per biological replicate were treated with dTAG7 or DMSO for 1 h or 4 h.

value: genome edited K562

value: chronic myelogenous leukemia

value: SSRP1 N-terminal dTAG

value: dTAG7 4h


title: PLZ_WT control Replicate 3

value: In vitro myotube

value: iPSC-derived myotubes


title: Rhesus Macaque DHAI collected at d3


title: WT_Ctl, rep 3, RNAseq

value: NK cells


title: K562, SSRP1-dTAG, MNase-seq, DMSO, rep2, 4h

value: DMSO 4h


title: PLZ_WT control Replicate 2

value: terminal differentiation


title: K562, SSRP1-dTAG, MNase-seq, dTAG7, rep1, 4h


title: Rhesus Macaque DHAI collected at d0

value: aIFNg


title: WT_Ctl, rep 2, RNAseq

value: Spleen


title: PLZ_WT control Replicate 1


title: K562, SSRP1-dTAG, MNase-seq, DMSO, rep1, 4h


title: KO_ChIP, rep 3, ChIPseq

data_processing:
Quality control of sequenced reads was assessed by FastQC (version 0.11.9). Cutadapt (version 4.1) was used to remove adapters sequences.Trimmed sequenced reads were aligned to the mouse reference genome (mm10) using Bowtie2 (version 2.3.4.1) and filtered with samtools (version 1.15.1).
Normalized coverage tracks (CPM normalization in bigWig format) were generated with bamCoverage from deepTools (version 3.4.2). The Integrative Genomic Viewer (version 2.10.2) (https://software.broadinstitute.org/software/igv/) was used to visualize peaks.
csaw (R package, version 1.28.0 was used to detect differentially bound sites (DBS) with sliding windows. Problematic regions in the mouse genome (mm10) were discarded using a curated blacklist downloaded from https://sites.google.com/site/anshulkundaje/projects/blacklists. Reads overlapping a sliding window across the genome were counted with windowCounts. The function normFactors was used to remove compositional biases and to perform count normalization. The resulting matrix of window's counts was analyzed with the voom method from the limma package.DBS were identified using a linear model with background (WT and KO) as predictor. Significant DBSs were selected with FDR <0.05.
Assembly: mm10
Supplementary files format and content: .bw

extract_protocol:
Cultured NK cells from Reg-1fl/fl and Reg-1ΔNK were cross-linked with formaldehyde (final concentration; 1%) followed by quenching with glycine. Wash the cells with PBS and resuspend the cell pellet with cell lysis buffer for ChIP and incubate for 10 min on ice. Pellet the cell nuclei by centrifugation, then resuspend the nuclear pellet in nuclei lysis buffer for ChIP followed by chromatin fragmentation with Bioruptor (Sonicbio Co., Ltd.).
Purified ChIP-DNA was applied for library preparation by DNA SMART ChIP-Seq Kit (TaKaRa) following the manufacturer’s instructions. Briefly, each 1 ng of purified ChIP-DNA demonstrated denaturation, dephosphorylation of 3’-Ends, and T-Tailing, then dsDNA was produced by Poly(dA) primer annealing and template-switching reaction. The obtained dsDNA was directly amplified into ChIP-seq libraries using SeqAmp DNA Polymerase and the forward and reverse primers from the Indexing Primer Set HT for Illumina followed by size selection using AMPure XP beads (Beckman Coulter), and 100-bp paired-end sequenced using a NovaSeq 6000 (Illumina).

value: OCT2 ChIP

value: KO


title: WT_Ctl, rep 1, RNAseq

value: control


title: HEK293_RNH1

value: Human embryonic kidney

value: wildtype

value: transfected with RNH1 plasmid, S9.6 antibody used


title: Rhesus Macaque DHEX collected at d28

value: DHEX


title: K562, SSRP1-dTAG, MNase-seq, dTAG7, rep2, 1h

value: genome edited K562

value: chronic myelogenous leukemia

value: dTAG7 1h


title: Rhesus Macaque DHEX collected at d14


title: HEK293_S9.6

value: S9.6 antibody used


title: Rhesus Macaque DHAI collected at d14

value: DHAI


title: Rhesus Macaque DHEX collected at d7


title: HEK293_FLAG_MCM8

value: transfected with FLAG-MCM8 plasmid, anti-FLAG antibody used


title: K562, SSRP1-dTAG, MNase-seq, DMSO, rep2, 1h

value: SSRP1 N-terminal dTAG

value: DMSO 1h


title: WT_ChIP, rep 3, ChIPseq

value: NK cells

value: WT


title: KO_Input, rep 3, ChIPseq

value: Spleen

value: input


title: K562, SSRP1-dTAG, MNase-seq, dTAG7, rep1, 1h


title: K562, SSRP1-dTAG, MNase-seq, DMSO, rep1, 1h


title: HEK293_Control

value: mouse IgG antibody


title: KO_ChIP, rep 2, ChIPseq

value: OCT2 ChIP

value: KO


title: K562, SSRP1-dTAG, 5cap-seq, dTAG7, rep2, 4h

data_processing:
The 5cap-seq reads were first trimmed of the UMI (first 8 nt of the reads) with UMI-tools and then trimmed with Cutadapt {Martin, 2011 #416} with options: -f fastq -q 30 -m 25 -O 13 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC followed by mapping to the human genome version GRCh38 merged with the D. melanogaster genome version Dm6 with the STAR mapper with options: --runThreadN 24 --readFilesCommand zcat --outFilterType BySJout --outFilterMultimapNmax 1 --alignEndsType Extend5pOfRead1 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.05 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate. We next deduplicated the mapped data with UMI-tools to remove any PCR duplicates based on the UMI sequences. We then identified the first transcribed base (5’ end of the RNA) and used only this position in downstream analyses. The spike-in reads (processed as above) that mapped to the D. melanogaster genome were too low to be used for robust normalization, so we used reads mapping to human genes to obtain normalization factors to correct for sequencing depth and therefore refrain from performing expression change analyses for this dataset.
Assembly: GRCh38
Supplementary files format and content: bigwig
Library strategy: 5cap-seq

extract_protocol:
RNA was extracted according to manufacturer's protocol. 5 μg of RNA was treated with 5 U of Turbo DNase (Ambion) for 20 min at 37 ºC. The RNA samples were then treated with 1 U of Terminator 5’-Phosphate-Dependent Exonuclease (Epicentre) for 60 min at 30 °C and purified by phenol:choroform:IAA extraction. rRNA-depleted RNA was treated with 30 U of quick CIP (NEB) for 30 min at 37 ºC and purified by double-phenol extraction and phenol:choroform:IAA extraction. CIP-treated RNA was then incubated with 5 U of Cap-CLIP acid pyrophosphatase (Cellscript) for 60 min at 37 ºC. Decapped-RNA samples were then purified by phenol:choroform:IAA extraction and ligated overnight at 16 ºC with an RNA adapter (10 μM) containing an 8-mer molecular barcode (UMI), 1 μl of T4 RNA ligase 1 and ATP (1 mM) for ligation to the 5’ ends of RNA. The following day, the samples were purified with 2X volume of RNAclean XP beads (Beckman Coulter) according to the manufacturer’s instructions followed by RNA fragmentation with NEBNext Magnesium RNA Fragmentation Module (NEB) for 5 min at 80 ºC, and immediately transferred on ice. Fragmented samples were purified with 3.5X volume of RNAclean XP beads and then incubated with random hexamers (Invitrogen) and dNTPs for 5 min at 65 °C, followed by incubation on ice. The RNA was reverse transcribed with Superscript II (Invitrogen) (25 °C for 10 min, 42 °C for 50 minutes, inactivation at 70 °C for 15 minutes). cDNA samples were purified with Ampure XP beads (Beckman Coulter). cDNA second-strand was synthesized with 0.5 μL of 5 μM biotinylated primer and Phusion High-Fidelity PCR Master Mix with HF Buffer (NEB) (1 min at 98 ºC, 2 min at 50 ºC and 15 min at 72 ºC), followed by purification using Ampure XP beads.
For library preparation the biotinylated samples were captured with 20 mL of streptavidin-coupled Dynabeads M-280 (Invitro- gen) by incubation for 30 min at room temperature on a rotating wheel. Double-stranded cDNA fragments were end-repaired with End Repair Enzyme Mix (NEB), dA-tailed with 7.5 U of Klenow Fragment (Thermo Scientific) and ligated to 0.5 mL of 2.5 mM paired-end sequencing adapters containing a multiplexing barcode with 800 U of T4 DNA ligase (New England BioLabs) for 2 hours at room temperature. Beads with bound cDNA were washed between each enzymatic reaction with wash buffer (5 mM Tris pH 7.5, 0.5 mM EDTA pH 8 and 1 M NaCl) with extra washes after ligation of the Illumina adaptor. The sample-bound beads were used for PCR amplification with 0.5 mL of 10 mM Illumina Paired-End primers and Phusion High-Fidelity PCR Master Mix with HF Buffer (NEB) with the following conditions: 30 s at 98_x0014_C for initial denaturation, followed by 10 cycles of 30 s at 98_x0014_C, 30 s at 65_x0014_C, 30 s at 72_x0014_C, and a final extension for 5 min at 72_x0014_C. The libraries were then purified using Ampure XP beads and analyzed with the Fragment Analyzer (NGS kit). Followed by pooling before size-selection with Ampure XP beads to enrich for fragments between 200 and 700 bp. The NGS libraries were sequenced on the Illumina NextSeq550 to generate 75-bp single- end reads.

treatment_protocol: 25 million cells per biological replicate were treated with dATG7 or DMSO for 1 h or 4 h. Next we spiked the samples D.melanogaster S2 cells (1:10) and performed subcellular fractionation as for mNET-seq. The chromatin pellets were treated with DNase I for 10 min before lysis in Qiazol (Qiagen).

value: dTAG7 4h


title: FixedRNA-BAL

description: 10X genomics

data_processing:
The Cell Ranger (v7.1.0) application (10x Genomics) was then used to demultiplex the BCL files into FASTQ files (cellranger mkfastq), to perform alignment (to Cell Ranger human genome references GRCh38), filtering and unique molecular identifier counting and to produce gene-barcode matrices.
Filtered matrix files were used for further scRNA-seq analyses with R Bioconductor (3.17) and Seurat
Assembly: GRCh38
Supplementary files format and content: barcode sequences corresponding to column indices
Supplementary files format and content: tsv files containing for each feature the feature ID, the name and the type of features (Gene, antibody)
Supplementary files format and content: mtx files describing the count of genes for all cells

source_name: Bronchoalveolar Lavage (BAL)

extract_protocol:
The Cells were fixed and barcoded using the Chromium Next GEM  Single Cell Fixed RNA Sample Preparation Kit for multiplexed samples.
A Gene Expression library was generated following the Chromium Fixed RNA Profiling workflow.

value: Lung


title: PBMC2_BCR

city: New Haven

first: Rong

last: Fan

state: CT

address: 55 Prospect Street

department: Department of Biomedical Engineering

institute: Yale University

data_processing:
The sequenced data was aligned and quantified using the CellRanger multi pipeline (version 7.0.0, 10x Genomics)
Assembly: GRCh38 human reference genome
Supplementary files format and content: Gene expression matrix
Supplementary files format and content: BCR expression matrix and clonotypes

source_name: PBMCs

growth_protocol: Cryopreserved PBMCs were thawed and the dead cell removal kit (Myltenyi Biotec) was applied to sort out dead cells. To enrich B cells, PBMCs were stained with anti-CD19 MicroBeads (Miltenyi Biotec) and loaded on a MACS Column that is placed in the magnetic field as per the manufacturer’s instructions.

extract_protocol:
Chromium Next GEM Single Cell 5' Reagent Kits v2 (10x Genomics) were employed to perform the multi-omics profiling of enriched B cells.
Libraries were built following the 10X Single Cell 5' Reagent Kits v2 protocol

value: PBMCs

tag: disease type

value: COVID patient with non-hematologic cancer

value: B cells


title: Rhesus Macaque DHGW collected at d14

value: DHGW

value: aIFNg


title: KO_ChIP, rep 1, ChIPseq


title: Rhesus Macaque DHGW collected at d7


title: K562, SSRP1-dTAG, 5cap-seq, DMSO, rep2, 4h

tag: cell line

value: genome edited K562

value: chronic myelogenous leukemia

value: DMSO 4h


title: Rhesus Macaque DHGW collected at d3


title: K562, SSRP1-dTAG, 5cap-seq, dTAG7, rep1, 4h

value: SSRP1 N-terminal dTAG


title: KO_Input, rep 2, ChIPseq

value: NK cells


title: PBMC1_BCR

value: COVID patient with chronic lymphocytic leukemia


title: PBMC2_GEX


title: KO_Input, rep 1, ChIPseq

value: Spleen

value: input


title: K562, SSRP1-dTAG, 5cap-seq, DMSO, rep1, 4h


title: Rhesus Macaque DHGW collected at d0


title: Rhesus Macaque DHEX collected at d0

value: DHEX


title: WT_ChIP, rep 2, ChIPseq

value: OCT2 ChIP

value: WT


title: Rhesus Macaque DHGW collected at d28


title: PBMC1_GEX


title: WT_Input, rep 3, ChIPseq


title: HepG2_SP2509

first: Boshi

last: Wang

address: No.800 Dongchuan Road

institute: Shanghai Cancer Institute

data_processing:
Raw RNA-seq data were subjected to quality control using FastQC (v0.11.9) and trimmed using Trim_galore (0.6.5-1).
SortMeRNA (4.2.0) was used to remove rRNA reads to generate clean data.
The clean reads were aligned to the human reference genome (hg38) using the HISAT2 (version 2.2.1) aligner to generate BAM files.
The aligned reads (BAM files) were transformed into bigwig files using Deeptools software (v3.5.1)
Assembly: hg38
Supplementary files format and content: bigwig

source_name: liver

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Life Technologies, CA, USA) according to the manufacturer's protocol, and RNA integrity was assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies, CA, USA) to obtain RIN values. RNA with RIN values > 7 was purified using an RNAClean XP Kit (Beckman Coulter, Inc. CA, USA) and RNase-Free DNase Set (QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using a VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, Nanjing, China), and sequencing was performed on an Illumina HiSeq 2500 system.

value: liver

value: HCC


title: K562, SSRP1-dTAG, 5cap-seq, dTAG7, rep2, 1h

value: dTAG7 1h


title: WT_ChIP, rep 1, ChIPseq


title: K562, SSRP1-dTAG, 5cap-seq, DMSO, rep2, 1h

value: DMSO 1h


title: Rhesus Macaque DHAD collected at d28

value: DHAD


title: Rhesus Macaque DHAD collected at d14


title: Rhesus Macaque DHAD collected at d7


title: HepG2_ctr

value: Control


title: K562, SSRP1-dTAG, 5cap-seq, dTAG7, rep1, 1h

value: genome edited K562


title: WT_Input, rep 2, ChIPseq


title: ovarian cancer_ov190161

city: shanghai

first: Wu

middle: yang

last: jun

address: shanghai dongan road 270

department: Fudan university shanghai cancer center

institute: Fudan university

data_processing:
Raw data were used Trimmomatic to remove reads which contain adapter, contain ploy-N and low quality
Clean data were mapped to hg38 using Hisat2(v2.0.5)
mapped reads were used Stringtie2 to assymble transcript
Gene and transcript count extra using prepDE.py
Assembly: hg38

source_name: primary ovarian tumor tissue

extract_protocol: 19 high-grade serous ovarian cancer  were used for RNA extraction and RNAseq. Total RNA was harvested using Trizol reagent. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA).  RNA libraries were prepared for sequencing using standard Illumina protocols

value: primary ovarian tumor tissue

tag: tumor stage(figo)

value: IVB

value: Optimal

value: High-grade serous ovarian cancer

tag: platinumstatus

value: Resistant

tag: recurrence

value: Yes


title: WT_Input, rep 1, ChIPseq

value: Spleen

value: input

tag: cell type

value: NK cells

tag: genotype


title: Rhesus Macaque DHAD collected at d3

tag: treatment


title: ovarian cancer_ov190146

tag: tissue

value: IIIC


title: Rhesus Macaque DHAD collected at d0


title: ovarian cancer_ov190130


title: K562, SSRP1-dTAG, mNET-seq, dTAG7, rep2, 4h

description: Pol II-associated RNA

data_processing:
The mNET-seq reads were trimmed with Cutadapt {Martin, 2011 #416} with options: -f fastq -q 30 -m 20 -O 13 -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC -A GATCGTCGGACTGTAGAACTCTGAAC followed by mapping to the human genome version GRCh38 merged with the yeast genome version SacCer3 with the STAR mapper {Dobin, 2013 #419} with options: --runThreadN 24 --readFilesCommand zcat --outFilterType BySJout --alignEndsType Extend5pOfReads12 --outFilterMatchNminOverLread 0.80 --outFilterMultimapNmax 1 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.02 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate. Duplicates were marked with Picard tools {Broad-Institute, 2019 #418}. We kept only uniquely mapped and properly paired reads to identify the last incorporated base (3’ end of the RNA), which is the first mapped base in read 2, and used only this position in downstream analyses. The counts for yeast genes were used to generate normalization factors with DESeq2 {Love, 2014 #420} to normalize the coverage profiles.
Assembly: GRCh38
Supplementary files format and content: bigwig

extract_protocol:
To isolate the chromatin, we followed the protocol as in Nojima, et al., 2016. The chromatin pellets were then washed with MNase buffer and digested with MNase (NEB) for 2 minutes at 37 °C. The reactions were then centrifuged to remove insoluble debris. The supernatant was diluted with 1:10 NET-2E buffer (50 mM Tris-HCl (pH 7.4, 150 mM NaCl, 0.05 % (vol/vol) NP-40 and 1 % Empigen BB). We added 50 µl of antibody-conjugated beads (Dynabeads M-280 Sheep Anti-Mouse IgG rebound with 30 µg anti-CTD antibody (Diagenode)) and incubated in the cold room for 1.5 h. The beads were 6 washes with NET-2E buffer and the RNA was phosphorylated at 5' RNA ends with T4 PNK 3’ phosphatase minus (NEB). We eluted the RNA with RNA extraction buffer (ZYMO Quick-RNA microPrep kit). S. cerevisae mRNA spike-ins were prepared as previously described Zumer et al, 2021. We added 1 ng of fragmented spike-in to the extraction buffer. Next, short immunoprecipitated RNA fragments were size selected (< 200 nt) and purified from the eluates according to the manufacturers protocol (ZYMO Quick-RNA microPrep kit) and eluted in 7.5 µl nuclease-free water.
NGS library preparation was done with Truseq small RNA kit (Illumina)

treatment_protocol: 50 million cells were treated per biological replicate sample.We trated the cells with dTAG7 or control: DMSO for 1 or 4 hours.

value: chronic myelogenous leukemia

value: SSRP1 N-terminal dTAG

value: dTAG7 4h


title: KO, ADT, L3

description: 10x Genomics

data_processing:
Cell ranger (version 6.0.0; 10x Genomics) was used to process single-cell data. In brief, cellranger mkfastq was used to output FASTQ files. Sequencing reads in FASTQ files were aligned to the mm10 Mouse genome using cellranger count and gene-by-cell matrices were generated for downstream analysis. Gene-by-cell matrices were analyzed using Seurat (R package, version 4.1.1) and other packages.
We normalized the count data with NormalizeData and selected the top 5,000 highly variable features. Features were scaled with ScaleData and principal component analysis (PCA) was calculated with RunPCA. The top 20 principal components were used to obtain Uniform Manifold Approximation and Projection (UMAP) scatterplots.
Clustering analysis was performed using the top 20 principal components to generate an SNN graph with FindNeighbors, and clusters were identified with the Leiden algorithm implemented in FindClusters with resolution of 0.6. Cluster-specific markers were identified using FindAllMarkers to select differentially expressed genes between each cluster and the average of all remaining clusters with the Wilcoxon Rank Sum test.
Differentially expressed genes were selected with an adjusted p-value cutoff of 0.01 and log2 fold change of 1.0 in absolute value (equivalent to a twofold change). For the integration of datasets, batch correction was performed with RunCanek from the Canek package (R package, version 0.2.1) using the top 5,000 highly variable features in each dataset.
Assembly: mm10
Supplementary files format and content: h5
Library strategy: CITE-seq

molecule: protein

extract_protocol:
Sorted splenic NK cells from Reg-1fl/fl and Reg-1ΔNK were washed twice with PBS and suspended in PBS supplemented with 400 μg/mL non-acetylated bovine serum albumin (Sigma Aldrich, B6917). Cells were labeled with selected oligo barcode conjugated antibodies.
Individual cells were then coupled to beads using the 10X Genomics Chromium controller (10X Genomics). Single-cell sequencing libraries were prepared following the 10X Genomics Protocol using 5’ Reagent Kits v2 chemistry and sequenced to a median depth of approximately 20,000 reads per cell using an Illumina NovaSeq 6000 on rapid run.

value: spleen

value: splenocytes

value: knock out


title: K562, SSRP1-dTAG, mNET-seq, DMSO, rep2, 4h

description: Pol II-associated RNA

value: genome edited K562

value: DMSO 4h


title: ovarian cancer_ov190055

value: primary ovarian tumor tissue


title: Rhesus Macaque DHFL collected at d28

value: DHFL


title: K562, SSRP1-dTAG, mNET-seq, dTAG7, rep1, 4h

description: Pol II-associated RNA


title: ovarian cancer_ov180065

value: Optimal

value: High-grade serous ovarian cancer


title: KO, ADT, L1

description: 10x Genomics


title: KO, ADT, L2

description: 10x Genomics


title: Rhesus Macaque DHFL collected at d7


title: ovarian cancer_ov170009

value: IVB

value: Resistant

value: Yes


title: Rhesus Macaque DHFL collected at d3


title: KO, GEX, L4

description: 10x Genomics


title: K562, SSRP1-dTAG, mNET-seq, dTAG7, rep2, 1h

description: Pol II-associated RNA

value: dTAG7 1h


title: ovarian cancer_ov170008

value: IIIC


title: Rhesus Macaque DHFL collected at d0


title: KO, GEX, L3

description: 10x Genomics


title: ovarian cancer_ov160219


title: K562, SSRP1-dTAG, mNET-seq, DMSO, rep2, 1h

description: Pol II-associated RNA

value: chronic myelogenous leukemia

value: DMSO 1h


title: KO, GEX, L2

description: 10x Genomics


title: Rhesus Macaque DHGJ collected at d14

value: DHGJ


title: K562, SSRP1-dTAG, 5cap-seq, DMSO, rep1, 1h

value: SSRP1 N-terminal dTAG


title: Rhesus Macaque DHFL collected at d14


title: KO, GEX, L1

description: 10x Genomics

value: spleen

value: splenocytes


title: ovarian cancer_ov170037

value: Sensitive


title: K562, SSRP1-dTAG, mNET-seq, DMSO, rep1, 1h

description: Pol II-associated RNA

value: genome edited K562


title: WT, ADT,L4

description: 10x Genomics

value: wild type


title: Rhesus Macaque DHGJ collected at d7


title: K562, SSRP1-dTAG, mNET-seq, DMSO, rep1, 4h

description: Pol II-associated RNA

value: DMSO 4h


title: WT, ADT,L3

description: 10x Genomics


title: K562, SSRP1-dTAG, TT-seq, labeled, dTAG7, rep2, 4h

description: fragmented 4sU-labeled RNA

data_processing:
TT-seq reads were trimmed with Cutadapt with options: -f fastq -q 30 -m 25 -O 13 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT, followed by mapping to the human genome version GRCh38 merged with the synthetic RNA spike-in sequences with the STAR mapper  with options: --runThreadN 24 --readFilesCommand zcat --outFilterType BySJout --outFilterMultimapNmax 1 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.02 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate. Duplicates were marked with Picard tools. We then kept only uniquely mapped and properly paired reads for the downstream analyses. The counts from spike-ins were then used to generate normalization factors (rCube) for the human gene counts and coverage profiles.
Assembly: GRCh38
Supplementary files format and content: bigwig

extract_protocol:
Six in vitro transcribed spike-in RNAs were added to the lysates (Qiazol, Qiagen) from 30 million cells, followed by extraction of RNA according to the manufacturer’s protocol.  This was followed by fragmentation by sonication and biotinylation of the 4sU-containing RNA. Two biotinylation reactions were set up per sample (150 µg fragmented total RNA, 10 mM Tris pH 7.5, 1 mM EDTA pH 8.0, 200 µg/ml HPDP-biotin, 40% DMSO) and then pooled after purification with the µMACS Streptavidin Kit (Miltenyi). The 4sU-labeled RNA was eluted by cleaving the HDPD-biotin with 100 mM DTT and then purified and concentrated with the miRNeasy Micro kit (Qiagen).
100 µg of the purified 4sU-labeled RNA was used as input for the Illumina stranded total RNA library prep kit (Illumina).

treatment_protocol: 30 million cells per biological replicate were treated with dTAG7 or DMSO (control) for 1 h or 4 h. We supplemented the treatment medium with 500 µM 4-thiouridine (4sU) and metabolically labeled the cells for 5 min. The cells were pelleted by 2 min 2000 rpm centrifugation and lysed in Qiazol (Qiagen).

value: dTAG7 4h


title: Rhesus Macaque DHGJ collected at d0


title: WT, ADT,L2

description: 10x Genomics


title: Rhesus Macaque DHGJ collected at d28


title: K562, SSRP1-dTAG, TT-seq, labeled, dTAG7, rep1, 4h

description: fragmented 4sU-labeled RNA


title: ovarian cancer_B10

value: primary ovarian tumor tissue

value: IIIB

value: Optimal

value: High-grade serous ovarian cancer


title: Rhesus Macaque DHMC collected at d28

value: DHMC


title: K562, SSRP1-dTAG, TT-seq, labeled, DMSO, rep1, 4h

description: fragmented 4sU-labeled RNA


title: K562, SSRP1-dTAG, mNET-seq, dTAG7, rep1, 1h

description: Pol II-associated RNA

value: dTAG7 1h


title: WT, ADT,L1

description: 10x Genomics


title: ovarian cancer_B9

value: IIIC

value: Yes


title: ovarian cancer_B2

value: Resistant


title: Rhesus Macaque DHMC collected at d14


title: K562, SSRP1-dTAG, TT-seq, labeled, dTAG7, rep2, 1h

description: fragmented 4sU-labeled RNA

value: chronic myelogenous leukemia

value: SSRP1 N-terminal dTAG


title: KO, ADT, L4

description: 10x Genomics

value: spleen

value: splenocytes

value: knock out


title: ovarian cancer_ov170028

value: IVB

value: Sensitive

value: NO


title: ovarian cancer_B8

value: primary ovarian tumor tissue


title: WT,GEX, L3

description: 10x Genomics

value: wild type


title: K562, SSRP1-dTAG, TT-seq, labeled, DMSO, rep2, 4h

description: fragmented 4sU-labeled RNA

value: genome edited K562

value: DMSO 4h


title: Rhesus Macaque DHGJ collected at d3

value: DHGJ


title: ovarian cancer_ov170018

value: Optimal

value: High-grade serous ovarian cancer


title: Rhesus Macaque DHMC collected at d3

value: DHMC


title: WT,GEX, L2

description: 10x Genomics


title: ovarian cancer_B7

value: IIIC


title: Rhesus Macaque DHMC collected at d0


title: Rhesus Macaque DHMC collected at d7


title: ovarian cancer_B6

value: IIIB

value: Yes


title: K562, SSRP1-dTAG, TT-seq, labeled, dTAG7, rep1, 1h

description: fragmented 4sU-labeled RNA

value: chronic myelogenous leukemia

value: SSRP1 N-terminal dTAG

value: dTAG7 1h


title: WT,GEX, L1

description: 10x Genomics

value: spleen

value: splenocytes


title: ovarian cancer_B4

value: Sensitive

value: NO


title: K562, SSRP1-dTAG, TT-seq, labeled, DMSO, rep1, 1h

description: fragmented 4sU-labeled RNA

value: DMSO 1h


title: Rhesus Macaque DHNA collected at d28

value: DHNA


title: K562, SSRP1-dTAG, NELF (Th1L), ChIP, dTAG7, rep2, 4h

data_processing:
ChIP-seq reads were aligned to human hg38 genome assembly merged with D.melanogaster genome using Bowtie 2 with the following parameters: -p 24 --no-discordant --no-mixed --very-sensitive. Duplicates were removed using Picard tools.
Assembly: GRCh38
Supplementary files format and content: bigwig

extract_protocol:
Cells were fixed with 1% formaldehyde (Thermo Scientific) for 8 min. 125 mM Glycine was added to quench the reaction and incubated for 5 min. A pellet containing 30 million cells was lysed with 5 mL of Farnham lysis buffer (5 mM Pipes pH 8.0, 85 mM KCl, 0.5% NP-40, 1x protease inhibitor (Sigma-Aldrich), 1x phosphatase inhibitor (Sigma-Aldrich)) for 10 min on ice. Nuclei pellet was resuspended with 1 mL of sonication buffer (10 mM Tris-HCl pH 7.5, 1mM EDTA, 0.4% SDS, 1x protease inhibitor, 1x phosphatase inhibitor) and incubated on ice for 10 min. Chromatin shearing was done using S220 Focused-ultrasonicator (Covaris) with following settings: duty cycle 5%, peak incident power 140W, cycle per burst 200, processing time 900 sec, bath temperature 6 °C, degassing mode continuous, water level (Run) 8.
ChIP-seq DNA library preparation was performed according to NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).

treatment_protocol: 30 million cells per biological replicate were treated with dTAG7 or DMSO (control) for 1 h or 4 h.

value: genome edited K562

value: dTAG7 4h

tag: chip antibody


title: WT,GEX, L4

description: 10x Genomics

value: wild type


title: KO_Sti, rep 3, ATACseq

data_processing:
Quality control of sequenced reads was assessed by FastQC (version 0.11.9). Cutadapt (version 4.1) was used to remove adapters sequences.
Trimmed sequenced reads were aligned to the mouse reference genome (mm10) using Bowtie2 (version 2.3.4.1) and filtered with samtools (version 1.15.1).
Normalized coverage tracks (CPM normalization in bigWig format) were generated with bamCoverage from deepTools (version 3.4.2).
Peaks were called with MACS (version 2.1.1.20160309) and loaded into R with rtracklayer package.Consensus peaks were calculated with reduce function in GenomicsRanges and reads mapping to the consensus peaks were computed with summarizeOverlaps function in GenomicAlignments.
Assembly: mm10
Supplementary files format and content: count.rds
Supplementary files format and content: bigwig and narrowPeak

extract_protocol:
NK cells were subjected to ATAC-seq analysis using ATAC-Seq Kit (Active Motif) following the manufacturer’s instructions (Active Motif). 100,000 cells were washed with PBS and resuspended in ATAC lysis buffer followed by Tagmentation reaction and purification.
Purified Tagmented DNA was amplified using a combination of indexed primers and resulting  libraries were purified again.

value: Spleen

value: NK cells

value: KO

value: stimulated with IL12/18


title: KO_Sti, rep 2, ATACseq


title: ovarian cancer_B3

value: primary ovarian tumor tissue

value: IIIC

value: Optimal

value: High-grade serous ovarian cancer

value: Yes


title: Non-Diabetic Foot Skin Donor #11 [N11]

city: luzhou

address: Zhong Shan Road

institute: SWMU

data_processing:
Paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq xten / NovaSeq 6000 sequencer (2 × 150bp read length).
The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2. The mapped reads of each sample were assembled by StringTie
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Non-diabetic foot skin

extract_protocol:
The total RNA was extracted from the tissue using TRIzol® Reagent according the standard procedure. RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: foot Skin

tag: disease

value: Non-diabetic


title: Rhesus Macaque DHNA collected at d7


title: K562, SSRP1-dTAG, NELF (Th1L), ChIP, DMSO, rep2, 4h

value: chronic myelogenous leukemia

value: SSRP1 N-terminal dTAG

value: DMSO 4h


title: Rhesus Macaque DHNA collected at d14

value: DHNA


title: K562, SSRP1-dTAG, TT-seq, labeled, DMSO, rep2, 1h

description: fragmented 4sU-labeled RNA

value: genome edited K562

value: DMSO 1h


title: KO_Sti, rep 1, ATACseq

value: Spleen


title: K562, SSRP1-dTAG, NELF (Th1L), ChIP, dTAG7, rep1, 4h

value: dTAG7 4h


title: KO_Ctl, rep 3, ATACseq

value: NK cells

value: KO

value: control


title: K562, SSRP1-dTAG, NELF (Th1L), ChIP, DMSO, rep1, 4h


title: Rhesus Macaque DHNA collected at d3


title: KO_Ctl, rep 2, ATACseq


title: K562, SSRP1-dTAG, NELF (Th1L), ChIP, dTAG7, rep2, 1h

value: dTAG7 1h


title: Rhesus Macaque DHNA collected at d0


title: Rhesus Macaque DHBA collected at d28

value: DHBA


title: Non-Diabetic Foot Skin Donor #8 [N8]


title: KO_Ctl, rep 1, ATACseq


title: K562, SSRP1-dTAG, NELF (Th1L), ChIP, DMSO, rep2, 1h


title: Non-Diabetic Foot Skin Donor #7 [N7]


title: Rhesus Macaque DHBA collected at d14


title: WT_Sti, rep 3, ATACseq

value: WT

value: stimulated with IL12/18


title: K562, SSRP1-dTAG, NELF (Th1L), ChIP, dTAG7, rep1, 1h


title: Non-Diabetic Foot Skin Donor #6 [N6]

value: foot Skin


title: WT_Sti, rep 2, ATACseq


title: K562, SSRP1-dTAG, NELF (Th1L), ChIP, DMSO, rep1, 1h


title: Non-Diabetic Foot Skin Donor #5 [N5]

value: Non-diabetic


title: Non-Diabetic Foot Skin Donor #4 [N4]


title: WT_Ctl, rep 3, ATACseq


title: WT_Sti, rep 1, ATACseq


title: Non-Diabetic Foot Skin Donor #3 [N3]


title: Rhesus Macaque DHBA collected at d0


title: K562, SSRP1-dTAG, Pol II, ChIP, dTAG7, rep2, 4h

value: chronic myelogenous leukemia

value: Rpb1 NTD antibody (CST, #14958)


title: Non-Diabetic Foot Skin Donor #2 [N2]


title: Rhesus Macaque DHMT collected at d28

value: DHMT


title: WT_Ctl, rep 1, ATACseq


title: Rhesus Macaque DHMT collected at d14


title: Non-Diabetic Foot Skin Donor #9 [N9]


title: K562, SSRP1-dTAG, Pol II, ChIP, DMSO, rep1, 4h

value: SSRP1 N-terminal dTAG

value: DMSO 4h


title: Rhesus Macaque DHBA collected at d7


title: K562, SSRP1-dTAG, Pol II, ChIP, dTAG7, rep1, 4h

value: genome edited K562


title: K562, SSRP1-dTAG, Pol II, ChIP, dTAG7, rep2, 1h


title: P19, shUbe2t #2, S9.6 (optimized)

first: Yongze

last: Yu

email: lwyyzsdu@163.com, lwyyzsdu@hotmail.com

state: Shandong

address: 文化西路44号国家辅助生殖与优生工程技术研究中心

data_processing:
The library preparations were sequenced on Illumina Novaseq platform at Novogene Science and Technology Co., Ltd (Beijing, China) and 150bp paired-end reads were generated
The read sequences produced by the Illumina pipeline in FASTQ format were pre-processed through Trimmomatic software, and all low-quality reads and PCR adapters were removed
CUT&Tag reads were aligned to the UCSC mm10 genome using Bowtie v0.7.12.
All peak calling was performed with MACS2 v2.1.2 using ‘macs2 -q 0.05 --call-summits --nomodel --shift -100 --extsize 200 --keep-dupall’.
bigWig files were generated using the genomicRanges R package. narrowPeak files were generated using MACS v2.1.2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

source_name: embryo

growth_protocol: α-MEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
The genome DNA were extracted by the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech, China; TD903).
CUT&Tag libraries were prepared using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech, China; TD903). Libraries were amplified using 11 cycles on the thermocycler. Libraries were purified with the AMPure beads and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: embryo

value: Mouse embryo carcinoma

value: Ube2t knockdown

value: Knockdown with shUbe2t #2 adenovirus, S9.6 antibody used


title: Diabetic Foot Skin Donor #10 [DW10]

source_name: Diabetic foot skin

value: diabetes


title: Rhesus Macaque DHBA collected at d3

value: control


title: Rhesus Macaque DHMT collected at d0


title: P19, shUbe2t #1, S9.6 (optimized)

address: 文化西路44号国家辅助生殖与优生工程技术研究中心

value: Knockdown with shUbe2t #1 adenovirus, S9.6 antibody used


title: Diabetic Foot Skin Donor #9 [DW9]


title: P19, shCtrl, S9.6 (optimized)

address: 文化西路44号国家辅助生殖与优生工程技术研究中心

value: Wild-type

value: Knockdown with control adenovirus, S9.6 antibody used


title: Diabetic Foot Skin Donor #8 [DW8]

value: foot Skin


title: WT_Ctl, rep 2, ATACseq

value: Spleen

value: NK cells

value: WT


title: Rhesus Macaque DHNC collected at d28

value: DHNC


title: K562, SSRP1-dTAG, Pol II, ChIP, dTAG7, rep1, 1h

value: chronic myelogenous leukemia

value: SSRP1 N-terminal dTAG

value: dTAG7 1h

value: Rpb1 NTD antibody (CST, #14958)


title: P19, shCtrl, No antibody (optimized)

address: 文化西路44号国家辅助生殖与优生工程技术研究中心

value: embryo

value: Mouse embryo carcinoma

value: Knockdown with control adenovirus, no primary antibody used


title: K562, SSRP1-dTAG, Pol II, ChIP, DMSO, rep1, 1h

value: genome edited K562

value: DMSO 1h


title: Diabetic Foot Skin Donor #7 [DW7]

value: diabetes


title: Rhesus Macaque DHNC collected at d14

value: control


title: Rhesus Macaque DHMT collected at d7

value: DHMT


title: dTAG_4hr_rep6

city: Goettingen

first: Abrar

last: Aljahani

address: Am Fassberg 11

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq550 output.
MCC pipeline (https://github.com/jojdavies/Micro-Capture-C)
ICE normalization (Imakaev et al. Nature Methods 2012)
Assembly: hg38
Supplementary files format and content: Chimeric junctions files: tab-delimited text files listing the locations of the identified valid junctions
Library strategy: Tiled-Micro-Capture-C (Tiled-MCC)

source_name: Bone Marrow

growth_protocol: RPMI-1640 (no glutamine), 10% fetal bovine serum, 1% GlutaMAX. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 2% formaldehyde for 10 minutes and permeabilised with 0.0025% digitonin. Chromatin was digested by MNase and religated. Decrosslinking and DNA extraction was performed. Samples were sonicated using a S220 focused-ultrasonicator (Covaris).
Tiled-Micro-Capture-C (Tiled-MCC) combines Micro-Capture-C (MCC) library preparation with oligonucleotide capture enrichment for deep, targeted sequencing of chromatin interactions within regions of interest. Details are described in the Methods section of the paper.

treatment_protocol: Cells were treated as described in the Methods section of the paper

value: Bone Marrow

value: Lymphoblast


title: Diabetic Foot Skin Donor #6 [DW6]

last: Jiang

value: foot Skin


title: Non-Diabetic Foot Skin Donor #1 [N1]

value: Non-diabetic


title: Non-Diabetic Foot Skin Donor #10 [N10]


title: Rhesus Macaque DHMT collected at d3

data_processing: Raw read counts were obtained from RCC files using the nSolver 4.0 Data Analysis software and the NS_NHP_Immunology_V2.0 rlf file references included with the nCounter NHP Immunology panel V2 kit.

extract_protocol: Cryopreserved BAL cells from pre-infection (d0) and days 3, 7, 14, and 28-35 post infection (necropsy) were thawed and homogenized using Qiagen RLT buffer Plus (Cat # 1053393) and QIAShredder Columns (Cat # 79656). RNA was isolated using the Qiagen RNeasy Mini kit (Cat # 74134) according to manufacturer’s instructions and eluted in 25uL of RNase free water. RNA was concentrated to 25-50ng/uL using Eppendorf Vacufuge plus centrifuge concentrator. RNA quality was confirmed with Agilent TapeStation. RNA was sent to the National Cancer Institute (NCI) Center for Cancer Research Genomics Core at the Frederick National Laboratory.